Salvacasani
Salvacasani
I am having the same issue! Did you ever figure out what the problem was? If not, I am happy to provide a sample with a subset of the alignment...
Here it is, I don't know how many of these should have ligated junctions, but there should be a good bunch. If there are no examples with separate mapping sites...
Hi! Have you been able to look into it? I tried to run it with the previous version of pairtools, but I get the same result.
Thank you for looking into it. I am still getting very strange results. This is the code that I am using pairtools parse2 --min-mapq 20 --single-end --max-inter-align-gap 30 --nproc-in 5...
Thanks I can reproduce this result. Since there is a multimaper (not sure why since I don't find it in the alignment) maybe this is not the best example. If...
Gotcha, Thank you so much for the help!!